Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 157

9 diseases · 17 shared-gene connections
9 Diseases
37 Unique genes
0.183 Avg. similarity score
Auditory neuropathy Most-connected disease (6 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Auditory neuropathy 6 6 31
Pendred syndrome 6 6 7
DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome 5 5 1
Sensorineural hearing loss thrombocytopenia syndrome 5 5 1
progressive microcephaly-seizures-cortical blindness-developmental delay syndrome 5 5 1
Neonatal convulsions 3 3 3
Arthrogryposis with ectodermal dysplasia 2 2 1
Deafness dystonia syndrome 1 1 1
hearing loss, autosomal recessive 116 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
DIAPH1 6 / 9 Auditory neuropathy, DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome, Neonatal convulsions, Pendred syndrome and 2 more
OTOF 3 / 9 Arthrogryposis with ectodermal dysplasia, Auditory neuropathy, Pendred syndrome
CLDN9 2 / 9 hearing loss, autosomal recessive 116, Pendred syndrome
MYO7A 2 / 9 Auditory neuropathy, Pendred syndrome
TIMM8A 2 / 9 Auditory neuropathy, Deafness dystonia syndrome
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Vitamin B2 (riboflavin) metabolism
SLC52A3, SLC52A2
 Reactome 2 / 7 92.7× 1.92e-4 3.79e-3 ✓ sig.
Defective SLC17A8 causes autosomal dominant deafness 25 (DFNA25)
SLC17A8
 Reactome 1 / 1 325× 3.08e-3 3.13e-2 ✓ sig.
Defective SLC26A4 causes Pendred syndrome (PDS)
SLC26A4
 Reactome 1 / 1 325× 3.08e-3 3.13e-2 ✓ sig.
Regulation of Apoptosis
OPA1
 Reactome 1 / 2 162× 6.15e-3 5.02e-2
Nicotine addiction
CACNA1A, SLC17A8
 KEGG 2 / 41 15.8× 7.02e-3 5.47e-2
TBC/RABGAPs
RAB33A, TBC1D24
 Reactome 2 / 46 14.1× 8.78e-3 6.34e-2
Parkinson disease
KIF5A, MFN2, ND6, TUBB4A
 KEGG 4 / 268 4.8× 8.98e-3 6.42e-2
RHO GTPases Activate Formins
DIAPH3, DIAPH1, TUBB4A
 Reactome 3 / 140 7.0× 9.02e-3 6.45e-2
Electron transport from NADPH to Ferredoxin
FDXR
 Reactome 1 / 3 108× 9.21e-3 6.53e-2
Potassium transport channels
KCNJ10
 Reactome 1 / 3 108× 9.21e-3 6.53e-2
Spinocerebellar ataxia
CACNA1A, OPA1, TWNK
 KEGG 3 / 144 6.8× 9.74e-3 6.75e-2
Retrograde endocannabinoid signaling
CACNA1A, ND6, SLC17A8
 KEGG 3 / 149 6.5× 1.07e-2 7.15e-2
Defective CYP11A1 causes Adrenal insufficiency, congenital, with 46,XY sex reversal (AICSR)
FDXR
 Reactome 1 / 4 81.1× 1.23e-2 7.74e-2
Kinesins
KIF5A, TUBB4A
 Reactome 2 / 59 11.0× 1.42e-2 8.41e-2
Huntington disease
KIF5A, ND6, TUBB4A, KCNJ10
 KEGG 4 / 308 4.2× 1.44e-2 8.52e-2

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
sensory perception of sound
OTOF, DIAPH3, MYO7A, SLC52A3, WFS1, DIAPH1, SLC17A8, ALDH7A1, SLC26A4
 GO:0007605 9 / 162 28.1× 2.23e-11 7.49e-9 ✓ sig.
riboflavin metabolic process
SLC52A3, SLC52A2
 GO:0006771 2 / 5 202× 3.80e-5 1.46e-3 ✓ sig.
riboflavin transport
SLC52A3, SLC52A2
 GO:0032218 2 / 6 168× 5.69e-5 1.98e-3 ✓ sig.
inner ear receptor cell differentiation
DIAPH3, MYO7A
 GO:0060113 2 / 9 112× 1.36e-4 3.80e-3 ✓ sig.
mitochondrial DNA replication
TWNK, POLG
 GO:0006264 2 / 11 91.8× 2.07e-4 5.18e-3 ✓ sig.
axonal transport of mitochondrion
NEFL, OPA1
 GO:0019896 2 / 12 84.2× 2.49e-4 5.90e-3 ✓ sig.
central nervous system myelination
PLP1, KCNJ10
 GO:0022010 2 / 16 63.1× 4.50e-4 8.90e-3 ✓ sig.
Rab protein signal transduction
RAB33A, RAB9B
 GO:0032482 2 / 17 59.4× 5.09e-4 9.68e-3 ✓ sig.
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
OPA1, WFS1
 GO:1902236 2 / 20 50.5× 7.09e-4 1.21e-2 ✓ sig.
mitochondrial fusion
MFN2, OPA1
 GO:0008053 2 / 21 48.1× 7.82e-4 1.29e-2 ✓ sig.
visual perception
MYO7A, OPA1, WFS1, KCNJ10
 GO:0007601 4 / 215 9.4× 8.36e-4 1.34e-2 ✓ sig.
microtubule polymerization
DIAPH3, TRPV4
 GO:0046785 2 / 25 40.4× 1.11e-3 1.61e-2 ✓ sig.
calcium ion import across plasma membrane
CACNA1A, TRPV4
 GO:0098703 2 / 28 36.1× 1.40e-3 1.84e-2 ✓ sig.
protein targeting to mitochondrion
MFN2, TIMM8A
 GO:0006626 2 / 29 34.8× 1.50e-3 1.91e-2 ✓ sig.
ectoderm and mesoderm interaction
TP63
 GO:0007499 1 / 1 505× 1.98e-3 2.24e-2 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Auditory neuropathy Pendred syndrome 0.083 3 2.57e-7 1.77e-6 ✓ sig.
DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome Sensorineural hearing loss thrombocytopenia syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome progressive microcephaly-seizures-cortical blindness-developmental delay syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
progressive microcephaly-seizures-cortical blindness-developmental delay syndrome Sensorineural hearing loss thrombocytopenia syndrome 0.500 1 6.49e-5 2.34e-4 ✓ sig.
DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome Neonatal convulsions 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Neonatal convulsions Sensorineural hearing loss thrombocytopenia syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
Neonatal convulsions progressive microcephaly-seizures-cortical blindness-developmental delay syndrome 0.250 1 1.95e-4 5.28e-4 ✓ sig.
DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome Pendred syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Arthrogryposis with ectodermal dysplasia Pendred syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
hearing loss, autosomal recessive 116 Pendred syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Pendred syndrome Sensorineural hearing loss thrombocytopenia syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Pendred syndrome progressive microcephaly-seizures-cortical blindness-developmental delay syndrome 0.125 1 4.55e-4 9.55e-4 ✓ sig.
Auditory neuropathy DIAPH1-related sensorineural hearing loss-thrombocytopenia syndrome 0.031 1 2.01e-3 2.89e-3 ✓ sig.
Auditory neuropathy Sensorineural hearing loss thrombocytopenia syndrome 0.031 1 2.01e-3 2.89e-3 ✓ sig.
Auditory neuropathy progressive microcephaly-seizures-cortical blindness-developmental delay syndrome 0.031 1 2.01e-3 2.89e-3 ✓ sig.
Auditory neuropathy Deafness dystonia syndrome 0.031 1 2.01e-3 2.89e-3 ✓ sig.
Arthrogryposis with ectodermal dysplasia Auditory neuropathy 0.031 1 2.01e-3 2.89e-3 ✓ sig.